PROJECT SUMMARY Hepatitis C virus (HCV) is a significant public health burden and co-infection with human immunodeficiency virus (HIV) is a critical area of investigation. Directly-acting antiviral (DAA) combination therapies have provided an opportunity to cure HCV infection at unprecedented rates. These therapies are limited primarily by cost and availability, making targeted treatment a potential unmet need. Approximately 30% of HCV mono- infected and 15% of HIV co-infected persons will clear HCV spontaneously after acute infection. Identifying human genetic variants that differentiate risk and rate of persistent HCV infection in these populations could provide new information to inform ?precision medicine? approaches to treatment, and will also shed light on new mechanistic pathways in HCV immunopathogenesis. A study including a PI and co-investigator on this proposal identified genetic variants in nuclear DNA loci for interferon responsiveness (IL-28B) and HLA class II (DQB) that explain 15% of the variation in spontaneous HCV clearance. While innate interferon-mediated immune responses and HLA are well-recognized factors in HCV immunology, less appreciated areas involve mitochondrial function and pathways, including mitochondrial antiviral signaling (MAVS), mitochondrial reactive oxygen species, mitophagy and mitochondria-associated apoptosis, and mitochondrial-associated ER membranes (MAM). Mitochondrial DNA (mtDNA) haplogroups are patterns of mtDNA single nucleotide polymorphisms that have been linked to differences in mitochondrial function and with HIV-related outcomes in studies led by the other PI and co-investigators on this proposal. While prior analyses have also identified associations between mtDNA haplogroups and outcomes in HIV/HCV co-infection, no studies to date have examined the role of mtDNA variants in HCV spontaneous clearance. We hypothesize that mtDNA haplogroups will have independent associations and/or interact with nuclear DNA variants known to predict HCV clearance, and these associations and/or interactions will be mediated by HIV co-infection We will test these hypotheses through multi-disciplinary expertise, the leveraging of rich existing genomic and clinical outcome data from >3800 HCV-infected persons (including >1300 with spontaneous HCV clearance and almost 800 HIV co-infected), and innovative methods to derive previously untapped mtDNA information. The aims of the proposal are to determine whether mtDNA haplogroups are associated with spontaneous HCV clearance in infected persons with and without HIV, and to determine whether mtDNA haplogroups further refine known associations between nuclear DNA genomic variants and spontaneous HCV clearance. These Aims will efficiently address gaps in our understanding of the role of mtDNA variation in HCV clearance, will provide mechanistic clues to the mitochondrial influence of HCV immunopathogenesis, and will lead to clinical studies of intervention strategies and therapeutics.